


Puella Magia Madoka Magica: Resonance

by Kiyomii



Category: Mahou Shoujo Madoka Magika | Puella Magi Madoka Magica
Genre: Alternate Universe, Other, Post-Rebellion Story
Language: English
Status: In-Progress
Published: 2018-09-24
Updated: 2018-09-24
Packaged: 2019-07-16 10:51:01
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 3,813
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/16084619
Author URL: https://archiveofourown.org/users/Kiyomii/pseuds/Kiyomii
Summary: In an alternate universe where Madoka exists as a human instead of a concept, the Incubators plan their counterattack against the Devil via creating a different Witch system. The only thing capable of stopping the Incubators is the same thing that helped them escape from the Devil, an Incubator technology surpassing the Soul Gems known as the Resonance Gems.





	1. Prologue

**Author's Note:**

> This is a story primarily based on expanding the backstory (my own interpretation) of the Incubators via Madoka's POV.

A feminine figure with cat-like ears and a tail collapsed onto a pile of scraps that used to be battleships and weapons. The biting cold of rusty metal gawned at her body, leaving behind only numbness when they were done.  
  
War had reduced this planet into an apocalyptic tragedy. Eight degrees off its original axis tilt. Erratic gravitational pull. Atmosphere completely stripped away by an enormous UASB meltdown during the war. The only life left here on a sub negative 200 Fahrenheit wasteland was her.  
  
For millions of years, she as an Incubator misdirected and manipulated young females from different planets across the galaxy into signing up as a magical girl and fight Witches in exchange for a wish. Those girls were all the same when they found out the truth behind the Witches. "You tricked us!" they would say, or some variation of it, angry and bitter. And then they got even more angry and bitter when she explained her reasoning for doing so. Their sacrifice was needed for the sake of this Universe that was running out of usable energy.  
  
She mustered whatever strength she had left and dropped the purple gem through a green portal. This gem was a Resonance Gem, its power limited only by the soul controlling it. Their solution to the Universe's energy crisis, as naive as it sounded, was to create something that would never run out of usable energy via their magical girl system. They would have succeeded in doing so by turning that Resonance Gem into an Infinity Gem, if it wasn't for the Devil.  
  
"Kaname Madoka, if you're out there somewhere, awaken and save the Universe from the Devil..."  
  
A black mist swirled at a distance. Numbness gave way to the biting cold again. Her last memories of being alive was the smile of Mistress Death mocking her for messing with powers she never completely understood.


	2. Chapter 1

Madoka awoke to a buzzing alarm in her bedroom. She had a strange dream where a dying cat lady was calling for her to save the Universe from the Devil.  
  
"I must've watched too much Kamen Rider with Tatsuya."  
  
Madoka pulled the curtains away to be greeted with a scenic forest view. Given the chance, she would love to become Sailor Moon or Kamen Rider Galaxy and save the Universe, but dreams were dreams for a reason.  
  
Madoka waved at her father watering the tomato plants in the garden below, "Good morning, Papa!"  
  
"Morning! If you don't mind, could you check on your mother to see if she's awake?"  
  
"Got it."  
  
Madoka went over to her mother's room and slammed open the door to see her three year old brother Tatsuya standing on the bed, about to perform his best imitation of a signature finishing move by the Kamen Riders he has recently been obsessed with.  
  
She chuckled. That won't be enough to wake Mama up.  
  
Madoka drew the curtains open before she pulled the blanket away from her mother.  
  
Her mother jumped out of the bed like a vampire exposed to sunlight before slowly turning to face them.  
  
"Good morning."  
  
===  
  
Madoka's mother grabbed a towel and wiped her face, "How's everything so far?"  
  
"Oh, Hitomi got a love letter again," said Madoka while brushing her teeth, "This makes two for the month already."  
  
"Pfft. Guys that don't have the guts to confess in person are absolutely worthless. She shouldn't waste her time on those kind of guys."  
  
By the time Madoka finished brushing her teeth, her mother was almost done with her makeup. She applied some final touches on her face with a powder puff before striking a confident pose at the mirror.  
  
"Perfect."  
  
Sometimes Madoka wondered if she was really the daughter of this incredible woman named Kaname Junko. Mama was always so fast, and so efficient. During breakfast, she could juggle between taking care of Tatsuya, reading the newspaper effortlessly, and finishing her food and cup of coffee. On the other hand, Madoka was sure she would end up in a complete mess if she attempted to do the same.  
  
"Umm... which ribbon should I pick?"  
  
The red one on her right, or the yellow on her left?  
  
"How about red?" said Junko.  
  
Madoka frowned, "Don't you think it might be a little too flashy?"  
  
"That's the point. Now all your secret admirers won't be able to resist you. I'm sure you'll get even more love letters than Hitomi."  
  
"Like I'd have any secret admirers."  
  
Secret admirer? There was nothing admirable about a girl like her. She was slow, clumsy, and didn't have any particular talents like playing the violin really well for example.  
  
"Confidence, Madoka. You have to believe in yourself. That's the secret in becoming a pretty girl with tons of admirers."  
  
If only being confident was that easy... nothing ever seemed easy for her anyway.  
  
===  
  
The afternoon sun's heat clung onto Madoka as she did some warm-up stretches at a soccer field. She never looked forward to PE lessons. Other than her general dislike towards exercising, she also hated being a huge burden in every team sports. At least Sayaka was on the same team with her for soccer.  
  
Madoka reluctantly wore a blue tag around her waist, "I'll just bring the whole team down." She could neither pass the ball properly, nor run fast enough to be useful.  
  
"Relax, it's just a friendly match," said Sayaka.  
  
"Still-"  
  
A whistle blow signalling the start of the match silenced her protest. Sayaka slapped her on the back with a reassuring smile, "Be confident!" before running off. There was no point in being confident when the chaos from nineteen athletic girls chasing after a ball left her confused and overwhelmed.  
  
A girl fired a cross towards Sayaka who followed up with a left shot into the goalpost.  
  
Madoka waved from a distance, "Good job!"  
  
"Thanks!" said Sayaka.  
  
Unlike her, Sayaka was really talented in sports. Unfortunately, she had zero talent in music, and her crush Kamijou Kyousuke was a violin prodigy. Sayaka once attempted to learn piano in hopes of being able to accompany Kyousuke's violin playing but it didn't work out so well for her.  
  
The match continued on. Madoka regretted not insisting on badminton. Some of her teammates shook their head as they ran past her. She must have looked like an complete idiot standing at a corner and not contributing anything to her team.  
  
The ball landed on her feet. A chance to finally contribute something! Okay, take a deep breath, just pass the ball to Sayaka and let her do her magic. Easy peasy.  
  
Madoka swerved behind with the ball. If Sayaka wasn't around, then the only thing left to do was to be confident and score. By some miracle, she kicked the ball inside the goalpost.  
  
"What's wrong?" said Madoka. Why were her fellow teammates so unenthusiastic about her goal? In fact, they seemed… upset at her. Sayaka for some reason was trying her best not to burst into laughter.  
  
"You kicked the ball into our goal," said one teammate before smacking her face with a palm.  
  
Madoka's face burned crimson red, "What?! Guys, I'm sorry! I thought I was facing the correct direction and-"  
  
"Don't worry about it, okay? We all make mistakes," said another teammate who was also a classmate of hers.  
  
"Yeah," said Sayaka, "It's just a friendly match, not the World Cup finals. Just relax and aim for the correct goalpost later."  
  
"Okay..."  
  
Being confident wasn't as hard as she thought. But it also wasn't something that would magically erase her ineptness.  
  
===  
  
Madoka, Sayaka and Hitomi were walking on a hillside path towards their usual cafe in the city area for dinner. School was finally over.  
  
Sayaka nudged Madoka with a grin, "Cheer up. At least you scored a goal. Even if it's an own goal."  
  
Even Hitomi could not help but suppress a chuckle, "And your team still won in the end, so it's alright."  
  
Madoka forced a smile as her face burned red with embarrassment again. Thank goodness Sayaka and the rest managed to score another goal after her terrible mistake, otherwise the guilt would torment her for days.  
  
A bicycle sped past a puddle of water, splashing water onto Hitomi's skirt.  
  
"I'll get you some tissue," offered Madoka, but to her horror she wasn't carrying her bag. "Oh no, I must have left my bag in class."  
  
"We'll wait for you here," said Hitomi.  
  
Madoka sprinted back to school, but her pace disappointingly dropped to a crawl after crossing the school gate. Eventually, she dragged herself to the classroom panting and retrieved her bag.  
  
The time displayed on the clock in class was 5.20pm. If she hadn't forgot her bag, the three of them would have already made it to the cafe before it was jam packed with students. Sometimes, all she ever wanted was to be just a little bit more useful to people instead of bringing them down.  
  
A shrill cry for help followed by the sound of plastic being hurled on the ground reverberated from the female toilet.  
  
"What a fucking weakling," said a female voice. Laughter from a group of girls followed soon after. It was Kikuchi Manami and her clique. Manami was a millionaire who supposedly had yakuza connections. Thus, the teachers would often ignore her bullying antics. It was said that whoever offended Manami can forget about having a peaceful school life until graduation day.  
  
"What are you waiting for? Save the girl from Manami!" said her inner Sayaka, but her inner Hitomi told her to get a teacher instead even if said teacher would probably pretend to be busy with work and just leave Manami to be. Wait, that wasn't her inner Hitomi. That was her cowardice speaking to her.  
  
Being confident wasn't hard, as she learned from the soccer match today. What's hard was making the right choice. If she offended Manami, it wasn't just her who would suffer under Manami's wrath. Her friends and the Gardening and Crafts Club would be implicated as well.  
  
"I'm so sorry for staring too long at you. Please just let me go," said a girl in between sobs. She must be Manami's victim.  
  
"I haven't had enough fun with you yet," said Manami.  
  
A sick gurgle escaped from the girl's throat.  
  
Madoka rushed into the toilet. Her worst fear came true. Manami was indeed strangling the poor girl while three other girls watched with glee.  
  
"Stop it! Why are you doing this to her?!" said Madoka.  
  
The three girls turned to face Madoka. "Are you standing up for this weakling over here?" said one girl. "If you don't want to become our enemy," said another girl as she raised a mop at Madoka, "then get the fuck out of here!"  
  
Manami chucked the pale, bespectacled girl aside like a girl bored of playing with her dolls, "I just hate the sight of her. That's all."  
  
"You can't just do this because you don't like how the way she looks. That's completely unreasonable," said Madoka. The pale, bespectacled girl who Manami was bullying fell unconscious. She had to get the girl to a doctor immediately.  
  
"I am being unreasonable. What are you going to do about it?"  
  
Manami's clique outnumbered her 4 to 1. There was no way she could get through them physically.  
  
"Please just let the poor girl off okay?" begged Madoka. That was all she could do. A sincere appeal, however clumsy, from the bottom of her heart  
  
Manami snapped her fingers, "That's it. You've wasted enough of my time listening to your crap."  
  
A girl stepped towards Madoka with a clenched fist. Madoka shut her eyes, body tense, ready for the bullying Manami's clique was about to unleash upon her.  
  
"Enough of this bullshit," said Sayaka.  
  
Madoka opened her eyes in surprise, "Sayaka?! What are you doing here?"  
  
"I should be the one asking you that. Hitomi and I were getting worried that something might have happened to you along the way."  
  
Manami looked at Sayaka with poorly veiled amusement, "I remember you two now. You're Hitomi's friends."  
  
"So what?" said Sayaka, "If you dare lay a hand on Hitomi, I'll beat the crap out of you and the disgusting leeches following you everyday."  
  
Manami held out a hand to stop the three girls from attacking Sayaka, "I'll give you one last chance for Hitomi's sake. Leave and pretend you saw nothing, or you'll be my next target."  
  
Hitomi wasn't very close to Manami, but apparently Hitomi's family had some business dealings with Manami, so Manami tended to spare students who were on close terms with Hitomi from her bullying.  
  
"I'm leaving with the girl," said Madoka with a level of determination she never knew existed within her, "She needs immediate medical care right now."  
  
Manami pushed Madoka aside with a smirk as her three other friends followed behind, "I hope you don't regret your decision, Kaname Madoka."  
  
===  
  
Central Mitakihara Park was a large park that Madoka passed through when she had to run some errands for Papa in the city area.  
  
"No one comes here at night," said Sayaka, "So if you feel... emboldened by your red ribbons, you could… yeah."  
  
"What do you mean by that?"  
  
"Don't act pure, you know what I mean. Remember that comic we read last year during a sleepover at my house?"  
  
"I don't..." Madoka's face flushed red in embarrassment, 'What?! No, no, no. I-I'm not going to do that with her!" That comic was an adult comic depicting a forbidden act of love between two girls. It also wasn't the only adult comic they read last year during that sleepover.  
  
Sayaka waved off her protest laughing as she left the park. Since Sayaka's house was too far from Homura's house, she decided to leave the responsibility to sending Homura home to her, who lived closer.  
  
Akemi Homura, the bespectacled girl bullied by Manami just now, might have been taller than her if she wasn't hunching her shoulders in fear all the time. It must be the trauma from Manami's bullying. The doctor said that Homura fainted from being too stressed out because of her weak heart, and that there was nothing to worry about other than taking her medications on time.  
  
Madoka sat at a bench before she felt a buzz in her pocket. It was a text message from Hitomi. _Don't worry about Manami, I'll talk to her tomorrow._  
  
Madoka texted back. _I'm so sorry for everything.  
  
There's no need to apologize. It's not your fault. Good night.  
  
Good night. Sweet dreams!_  
  
Madoka gestured for Homura to sit beside her. Homura nodded and slowly took a seat beside her. The starry night was like a black canvas adorned by tiny glittering diamonds.  
  
"Beautiful night, isn't it?" said Madoka. Looking at Homura reminded her of herself when she was in fifth grade. Quiet and nervous around people. Being in a new environment always made her feel like this. Fortunately, she met Sayaka, and then in seventh grade, she met Hitomi and life has been pretty fun so far being with the two of them.  
  
"Why did you save me from them?" Homura burst into tears, "Those bullies aren't going to let you off easily! All your friends are going to leave you! I'm… not worth it!"  
  
Madoka fumbled for a piece of tissue from her bag, "No one deserves to be bullied. No one."  
  
"But…"  
  
"Have some confidence in yourself. You're worth it."  
  
Homura wiped her tears with the tissue Madoka offered her, "I'm sorry."  
  
Madoka patted Homura's back, "You don't have to apologize, it's not your fault at all. It's Manami's fault for bullying you." She was also at fault for almost abandoning Homura. Her cowardice sickened her. Afraid of offending Manami, afraid of becoming a murderer if Manami actually strangled Homura to death, and afraid of telling Homura the truth. She was not a hero like Sayaka. Sayaka would have acted immediately even if it's Manami, consequences be damned and all.  
  
The look of awe and respect Homura gave her was almost a torture by itself. A coward like her deserved none of it.  
  
They continued their journey. There was still quite a distance from the train station even after passing through Central Mitakihara Park. Turn right afterwards, and Homura should be home.  
  
"Would you like to join us for dinner tomorrow night? There's a new cafe Hitomi wanted to go tomorrow downtown," said Madoka.  
  
Homura stammered. It seemed like there was something she wanted to say, but had difficulty into putting it to words. "... I'd just be trouble for everyone." was what she finally managed to say.  
  
"Please don't say that! Hitomi said she'd talk to Manami, so everything's going to be okay."  
  
"No, it's not about Manami. I'm… someone who can't do anything right. I'm also a boring person who doesn't talk much, so I'd just be an eyesore if I joined your friends for dinner."  
  
"I'm sure they'll like you, I promise! I know that because I was like you when I was in fifth grade. I thought I wasn't going to make any friends, but then I met Sayaka and Hitomi. Trust me, you're going to be just fine."  
  
Homura nodded meekly.  
  
"So… is that a yes?" said Madoka.  
  
"I'll do my best."  
  
Madoka slapped Homura on the back playfully, "That's the spirit." It was a very Sayaka thing she did that elicited a smile from Homura. Homura was finally smiling. Tomorrow is going to be so much fun with Homura joining them.  
  
The beautiful night sky twisted and warped into a red canvas scribbled with white curly lines while the streets faded into a desolate world haphazardly plastered with renaissance artworks.  
  
"Madoka, wh-where are we?" said Homura.  
  
Madoka grabbed hold of Homura's trembling hands with a smile, "I don't know, but we'll get out of here somehow."  
  
The ground beneath them was uneven, and painted with various abstract figures one could find in the artworks of Pablo Picasso and Salvador Dali.  
  
"Aren't you… afraid?"  
  
"As long as you don't lose hope, there's nothing to be afraid at all."  
  
Just what was going on? How did the streets turn into this bizarre place? Surely she and Homura would find an exit if they just keep walking. That was frankly the only thing they could do.  
  
Homura winced, "Um, I think you're holding my hand a little too hard..."  
  
A silver astylar monument popped up together with three artwork-like monsters scuttling towards them.  
  
"Run!" said Madoka.  
  
More and more monsters appeared as they ran. Those monsters looked familiar. They looked almost like the abstract figures painted on the ground.  
  
Homura let out a scream as her legs gave way. She clutched at her chest in agony.  
  
"Wh-What's wrong?!" said Madoka. This was the worst time to collapse in pain.  
  
"Medicine... my medicine..."  
  
Madoka frantically searched her body for any medication, "I can't find anything!"  
  
Homura screamed again, the clutching at her chest grew tighter.  
  
Madoka blinked back tears as she tried to find something on Homura again. She had to be faster than the monsters! Does it really matter if she found Homura's medication before the monsters? Those monsters were actually appearing from the ground itself! Unless she could fly, the monsters were going to get them eventually! They were all going to die in this wretched artsy place!  
  
The monsters were less than a feet away from them.  
  
This was it.  
  
Mundane memories of her life flashed right before her. Papa was watering the tomatoes while Tatsuya would try to grab one with his little hands. Tatsuya wasn't going to eat it of course. He hurled them at the windows, clapping each time he successfully landed a hit. And then Mama would clean up the mess with her while Papa lectured Tatsuya about the importance of not wasting food.  
  
Her next memory was about Sayaka describing in great detail to Hitomi about the forbidden acts done by two girls inside the comic they read last year. Hitomi covered her ears as her face flushed even redder than Papa's tomato, upset that Sayaka would actually read such a comic. It was hilarious to see a normally dignified Hitomi being so flustered.  
  
The monsters were now right next to them.  
  
Goodbye, everyone.  
  
A red blur sliced the monsters into pieces before a glowing red spear struck the monument. After a huge explosion, the bizarre world faded back into their reality.  
  
In front of her was an armored figure. The sleek red armor looked like it belonged to an outer space movie, the kind of movie Sayaka would love to watch. No, it looked more like the Bleeding Edge armor Sayaka showed her the other time from Iron Man, but the figure's mask was completely black with no facial features.  
  
The armor disintegrated into hexagon pixels, revealing her savior as a girl with red ponytail. "Don't just look at me like an idiot!" she snapped, "Perform CPR on the girl while I go get the ambulance."  
  
Madoka hurried over to Homura and pressed down hard on her chest, "Please be okay... Please..."  
  
They still had a dinner date tomorrow.  
  
===  
  
The doctor had a grave expression as he exited the ER room.  
  
Madoka took a deep breath, "So how's Homura?" She was prepared for the worst. The stress from Manami was enough to knock Homura unconscious. Not to mention something out of the world like being attacked by a Witch.  
  
"I'm sorry. We did our best, but we were unable to revive her."  
  
"I see. Thank you."  
  
Madoka sank back to her chair, tears dripping down her cheeks. There was no point in crying. Homura was dead, and nothing would change that fact.  
  
"I'd advise you to just forget all about the Witches," said Kyoko. "There's nothing you and I can do anyway."  
  
The girl who saved her and Homura from the Witch was Sakura Kyoko. She said that the monsters that attacked them just now were the minions of a Witch while the silver monument was the Witch itself. Once inside that bizzare world which was actually the barrier of a Witch, the only way out was to destroy the Witch.  
  
"Homura just died because of the Witch! I can't just forget about it!"  
  
Kyoko was unfazed by Madoka's outburst, "You kill one Witch, ten more Witches appears as a replacement. No matter how hard we try, people are still going to die from Witches. I'm sorry that it had to be your friend Akemi Homura, but I guess that's life."  
  
"Maybe we could target the source and d-"  
  
Kyoko shot a glare at Madoka, "Don't even think about it. If you still cherish your ordinary life as a middle schooler, please, just forget about the Witches."  
  
"I..."  
  
Before Madoka could finish, Kyoko left the hospital.  
  
"...don't know if I can."


End file.
